NEUROG2

gene
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Also known as Atoh4Math4Angn-2bHLHa8NGN2

Summary

NEUROG2 (neurogenin 2, HGNC:13805) is a protein-coding gene on chromosome 4q25, encoding Neurogenin-2 (Q9H2A3). Transcriptional regulator.

This gene encodes a neural-specific basic helix-loop-helix (bHLH) transcription factor that can specify a neuronal fate on ectodermal cells and is expressed in neural progenitor cells within the developing central and peripheral nervous systems. The protein product of this gene also plays a role in the differentiation and survival of midbrain dopaminergic neurons.

Source: NCBI Gene 63973 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 30 total
  • Transcription factor: yes — 27 downstream targets (CollecTRI)
  • MANE Select transcript: NM_024019

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13805
Approved symbolNEUROG2
Nameneurogenin 2
Location4q25
Locus typegene with protein product
StatusApproved
AliasesAtoh4, Math4A, ngn-2, bHLHa8, NGN2
Ensembl geneENSG00000178403
Ensembl biotypeprotein_coding
OMIM606624
Entrez63973

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000313341

RefSeq mRNA: 1 — MANE Select: NM_024019 NM_024019

CCDS: CCDS3698

Canonical transcript exons

ENST00000313341 — 2 exons

ExonStartEnd
ENSE00001212603112515847112516180
ENSE00001212610112513516112515476

Expression profiles

Bgee: expression breadth broad, 43 present calls, max score 97.24.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.8826 / max 204.6808, expressed in 134 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
536530.8826134

Top tissues by expression

268 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
ganglionic eminenceUBERON:000402397.24gold quality
ventricular zoneUBERON:000305394.33gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099191.94gold quality
cortical plateUBERON:000534387.30gold quality
embryoUBERON:000092278.71gold quality
right hemisphere of cerebellumUBERON:001489059.26gold quality
cerebellar cortexUBERON:000212958.68gold quality
cerebellar hemisphereUBERON:000224558.41gold quality
putamenUBERON:000187458.38gold quality
gluteal muscleUBERON:000200058.35gold quality
triceps brachiiUBERON:000150958.16gold quality
cerebellumUBERON:000203757.50gold quality
amygdalaUBERON:000187656.40gold quality
caudate nucleusUBERON:000187355.46gold quality
Ammon’s hornUBERON:000195454.13gold quality
cerebellar vermisUBERON:000472053.01gold quality
pancreatic ductal cellCL:000207951.23silver quality
prefrontal cortexUBERON:000045150.93gold quality
Brodmann (1909) area 46UBERON:000648349.93gold quality
epithelial cell of pancreasCL:000008349.68gold quality
temporal lobeUBERON:000187149.38gold quality
cervix squamous epitheliumUBERON:000692249.20gold quality
hair follicleUBERON:000207349.18gold quality
olfactory bulbUBERON:000226448.92gold quality
myocardiumUBERON:000234948.87gold quality
type B pancreatic cellCL:000016948.83gold quality
cingulate cortexUBERON:000302748.81gold quality
anterior cingulate cortexUBERON:000983548.81gold quality
quadriceps femorisUBERON:000137748.64gold quality
cardiac muscle of right atriumUBERON:000337948.55gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-10485yes544.08
E-MTAB-8894yes400.34
E-HCAD-5yes20.64
E-ANND-3no1.31

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

27 targets.

TargetRegulation
ASCL1Repression
ATOH7
BTG2Activation
CCND1Repression
CCNE2Repression
DLK1Repression
DLL1Activation
DLL3Activation
ELAVL4Activation
EOMESActivation
ETV1Repression
FEZF1
FEZF2
HES1
JAG2Activation
MEG8Repression
NEUROD1Activation
NEUROD4Activation
NEUROG2
PAX3
PAX6Repression
PCSK6
RAP1B
RND2Activation
RTL1Repression
SIRT1
ZBTB18Activation

JASPAR motifs

MotifNameFamily
MA0669.1NEUROG2Tal-related
MA1642.1NEUROG2Tal-related
MA1642.2NEUROG2Tal-related

JASPAR matrix evidence (PMIDs): PMID:19389376

Upstream regulators (CollecTRI, top): ATOH7, BMP7, CTNNB1, ESR1, FEZF1, FGF19, FOXA1, FOXA2, HES1, HES5, HEYL, LMX1A, NEUROD1, NEUROG1, NEUROG2, NEUROG3, OTX2, PAX3, PAX6, SOX2, TCF3, UNCX, ZBTB18

miRNA regulators (miRDB)

109 targeting NEUROG2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-5692A100.0074.406850
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-188-3P100.0068.761240
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-126-5P100.0072.713180
HSA-MIR-340-5P100.0072.504437
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-10401-5P99.9965.79948
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-381-3P99.9371.872854
HSA-MIR-30099.9271.762856
HSA-MIR-10523-5P99.9169.222038
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-374A-5P99.9071.342923

Literature-anchored findings (GeneRIF, showing 14)

  • expression of Ngn2 during the differentiation of neuronl human embryo stem cells. (PMID:17784840)
  • Rat and mouse species-dependent differences of Nurr1 and Ngn2 actions in dopamine neuron differentiation. (PMID:18242186)
  • Novel compound heterozygous variants (Gly56Arg and Asp206Glu) were found in a 91-year normal male, suggesting that mutations in the coding region of the NEUROG2 gene play little or no role in the development of PD. (PMID:19879328)
  • human embryonic progenitors expressing neurogenin-2 stimulate axonal sprouting and improve motor recovery after severe spinal cord injury (PMID:21209909)
  • Results show that neurogenin-1 and -2 drive homogeneous differentiation of human stem cells into bipolar neurons in 4 days in defined media. (PMID:25403753)
  • Study shows neurogenin 2 enhances the generation of patient-specific induced neuronal cells. (PMID:25912433)
  • combining NGN2 programming with SMAD and WNT inhibition generates human patterned induced neurons (PMID:29791859)
  • HOTAIRM1 regulates neuronal differentiation by modulating NEUROGENIN 2 and the downstream neurogenic cascade. (PMID:32661334)
  • Generation and optimization of highly pure motor neurons from human induced pluripotent stem cells via lentiviral delivery of transcription factors. (PMID:32783653)
  • MiR-211 determines brain metastasis specificity through SOX11/NGN2 axis in triple-negative breast cancer. (PMID:33536579)
  • NGN2 induces diverse neuron types from human pluripotency. (PMID:34358451)
  • Cend1 and Neurog2 efficiently reprogram human cortical astrocytes to neural precursor cells and induced-neurons. (PMID:34549796)
  • Neurogenin-2 induced neuronal differentiation in co-cultured bone marrow stromal and neonatal cortical cells. (PMID:38385475)
  • Generation of human excitatory forebrain neurons by cooperative binding of proneural NGN2 and homeobox factor EMX1. (PMID:38446849)

Cross-species orthologs

11 orthologs

OrganismSymbolGene ID
mus_musculusNeurog2ENSMUSG00000027967
rattus_norvegicusNeurog2ENSRNOG00000010972
drosophila_melanogasteramosFBGN0003270
drosophila_melanogasteratoFBGN0010433
drosophila_melanogastertapFBGN0015550
drosophila_melanogasterOliFBGN0032651
caenorhabditis_elegansWBGENE00001961
caenorhabditis_elegansWBGENE00003018
caenorhabditis_elegansWBGENE00003595
caenorhabditis_elegansWBGENE00009540
caenorhabditis_elegansWBGENE00013665

Paralogs (15): NEUROG3 (ENSG00000122859), NEUROD4 (ENSG00000123307), BHLHE23 (ENSG00000125533), NEUROD1 (ENSG00000162992), NEUROD6 (ENSG00000164600), ATOH8 (ENSG00000168874), NEUROD2 (ENSG00000171532), ATOH1 (ENSG00000172238), OLIG3 (ENSG00000177468), ATOH7 (ENSG00000179774), BHLHA15 (ENSG00000180535), BHLHE22 (ENSG00000180828), NEUROG1 (ENSG00000181965), OLIG1 (ENSG00000184221), OLIG2 (ENSG00000205927)

Protein

Protein identifiers

Neurogenin-2Q9H2A3 (reviewed: Q9H2A3)

Alternative names: Class A basic helix-loop-helix protein 8, Protein atonal homolog 4

All UniProt accessions (1): Q9H2A3

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional regulator. Involved in neuronal differentiation. Activates transcription by binding to the E box (5’-CANNTG-3’).

Subunit / interactions. Efficient DNA binding requires dimerization with another bHLH protein.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_076924* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR011598bHLH_domDomain
IPR032655Ngn-2_bHLHDomain
IPR036638HLH_DNA-bd_sfHomologous_superfamily
IPR050359bHLH_transcription_factorsFamily

Pfam: PF00010

UniProt features (5 total): region of interest 2, chain 1, domain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H2A3-F164.980.27

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 137 (showing top): AHRARNT_01, chr4q25, TAATAAT_MIR126, BENPORATH_ES_WITH_H3K27ME3, TGCACTT_MIR519C_MIR519B_MIR519A, GCANCTGNY_MYOD_Q6, TTTGTAG_MIR520D, GOBP_NEUROGENESIS, TGACCTY_ERR1_Q2, GOBP_FOREBRAIN_DEVELOPMENT, ATGTTAA_MIR302C, COUP_01, GOBP_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION, HNF4_DR1_Q3, HNF4_01

GO Biological Process (7): sensory organ development (GO:0007423), forebrain development (GO:0030900), positive regulation of transcription by RNA polymerase II (GO:0045944), obsolete positive regulation of DNA-binding transcription factor activity (GO:0051091), axon development (GO:0061564), nervous system development (GO:0007399), cell differentiation (GO:0030154)

GO Molecular Function (6): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), protein dimerization activity (GO:0046983), E-box binding (GO:0070888), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of transcription by RNA polymerase II2
animal organ development1
brain development1
anatomical structure development1
transcription by RNA polymerase II1
positive regulation of DNA-templated transcription1
neuron projection development1
system development1
cellular developmental process1
chromatin1
RNA polymerase II transcription regulatory region sequence-specific DNA binding1
DNA-binding transcription factor activity1
protein binding1
RNA polymerase II cis-regulatory region sequence-specific DNA binding1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
binding1
chromosome1
cellular anatomical structure1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1632 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NEUROG2ASCL1P50553971
NEUROG2PAX6P26367901
NEUROG2ISL1P20663891
NEUROG2LHX3Q9UBR4889
NEUROG2LMX1AQ8TE12871
NEUROG2SOX1O00570862
NEUROG2SOX2P48431841
NEUROG2POU4F1Q01851827
NEUROG2OLIG2Q13516813
NEUROG2LHX1P48742804
NEUROG2RND2P52198795
NEUROG2ISL2Q96A47794
NEUROG2LDB1Q86U70773
NEUROG2LHX2P50458749
NEUROG2SOX3P35714746

IntAct

6 interactions, top by confidence:

ABTypeScore
PFDN5NEUROG2psi-mi:“MI:0915”(physical association)0.560
NEUROG2Dlg4psi-mi:“MI:0407”(direct interaction)0.440
TCF4HMGB1psi-mi:“MI:0914”(association)0.350
PFDN5NEUROG2psi-mi:“MI:0915”(physical association)0.000

BioGRID (9): NEUROG2 (Synthetic Growth Defect), NEUROG2 (Two-hybrid), NEUROG2 (Negative Genetic), NEUROG2 (Cross-Linking-MS (XL-MS)), NEUROG2 (Affinity Capture-MS), NEUROG2 (Affinity Capture-MS), NEUROG2 (Affinity Capture-MS), NEUROG2 (Affinity Capture-MS), NEUROG2 (Affinity Capture-Western)

ESM2 similar proteins: A6NEQ2, A7MB34, A8MYZ6, O02754, O02755, O02756, O15522, O35392, O60548, O70191, O70220, O77728, P05554, P16443, P17542, P17676, P21272, P22091, P28033, P49715, P49716, P53566, P54845, P70447, Q00322, Q03484, Q10586, Q13461, Q15744, Q32PF6, Q5PQP0, Q5T953, Q60843, Q60925, Q63244, Q6P788, Q70KY4, Q7RTS3, Q8N350, Q8NDY6

Diamond homologs: A8E5T6, B6VQA1, O09029, O09105, O13125, O13126, O16867, O35437, O42202, O42606, O43680, O45489, O57598, O88940, O96004, O96642, P10627, P13903, P46581, P48985, P48986, P48987, P57100, P57101, P57102, P59101, P61295, P61296, P70447, P70562, P70595, P70660, P70661, P79765, P79766, P79782, P79920, P97832, Q08DI0, Q0V9X5

SIGNOR signaling

4 interactions.

AEffectBMechanism
NEUROG3“down-regulates quantity by repression”NEUROG2“transcriptional regulation”
HES1“down-regulates quantity by repression”NEUROG2“transcriptional regulation”
HES5“down-regulates quantity by repression”NEUROG2“transcriptional regulation”
NEUROG2up-regulatesNeurogenesis

Disease & clinical

Clinical variants and AI predictions

ClinVar

30 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance29
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

122 predictions. Top by Δscore:

VariantEffectΔscore
4:112515472:ACATC:Aacceptor_gain1.0000
4:112515473:CATC:Cacceptor_gain1.0000
4:112515473:CATCC:Cacceptor_gain1.0000
4:112515475:TC:Tacceptor_gain1.0000
4:112515476:CC:Cacceptor_gain1.0000
4:112515477:CT:Cacceptor_loss1.0000
4:112515478:T:Cacceptor_loss1.0000
4:112515481:C:CTacceptor_gain1.0000
4:112515846:CTTA:Cdonor_gain1.0000
4:112515474:ATC:Aacceptor_gain0.9900
4:112515477:C:CCacceptor_gain0.9900
4:112515477:C:Tacceptor_gain0.9900
4:112515481:C:Tacceptor_gain0.9900
4:112515482:G:Tacceptor_gain0.9900
4:112515843:TTAC:Tdonor_loss0.9900
4:112515845:A:ACdonor_gain0.9900
4:112515845:ACTTA:Adonor_loss0.9900
4:112515846:C:CCdonor_gain0.9900
4:112515846:CT:Cdonor_gain0.9900
4:112515846:CTT:Cdonor_gain0.9900
4:112515846:CTTAG:Cdonor_gain0.9900
4:112515850:G:Cdonor_gain0.9800
4:112515842:CTTA:Cdonor_gain0.9500
4:112515849:A:ACdonor_gain0.9500
4:112515841:A:ACdonor_gain0.8900
4:112515842:C:CCdonor_gain0.8900
4:112515865:G:Adonor_gain0.8800
4:112515809:C:CTdonor_gain0.8300
4:112515348:T:TAdonor_gain0.7700
4:112515810:C:CTdonor_gain0.7600

AlphaMissense

1720 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:112514985:A:GL164P1.000
4:112514985:A:TL164H1.000
4:112514994:A:CI161S1.000
4:112514994:A:GI161T1.000
4:112514994:A:TI161N1.000
4:112514997:T:CY160C1.000
4:112514998:A:CY160D1.000
4:112514998:A:GY160H1.000
4:112515006:G:TA157D1.000
4:112515009:A:GF156S1.000
4:112515012:C:GR155P1.000
4:112515015:A:CL154R1.000
4:112515015:A:GL154P1.000
4:112515015:A:TL154Q1.000
4:112515021:T:AE152V1.000
4:112515024:A:CI151S1.000
4:112515024:A:TI151N1.000
4:112515026:C:AK150N1.000
4:112515026:C:GK150N1.000
4:112515027:T:AK150M1.000
4:112515028:T:CK150E1.000
4:112515028:T:GK150Q1.000
4:112515030:G:AT149I1.000
4:112515033:A:GL148P1.000
4:112515057:G:TP140H1.000
4:112515058:G:AP140S1.000
4:112515060:A:TL139H1.000
4:112515070:G:TR136S1.000
4:112515072:A:GL135P1.000
4:112515072:A:TL135Q1.000

dbSNP variants (sampled 300 via entrez): RS1000782099 (4:112515422 C>A), RS1000990135 (4:112514837 C>T), RS1001897165 (4:112514511 G>A,T), RS1001983168 (4:112515812 C>A,T), RS1002963445 (4:112517060 A>C), RS1004470346 (4:112515203 G>A), RS1005210649 (4:112516090 T>C), RS1005445259 (4:112513663 G>A), RS1006887143 (4:112516747 T>G), RS1007170239 (4:112516594 C>A,G), RS1007948197 (4:112517602 T>C,G), RS1008171228 (4:112517969 G>A), RS1008536444 (4:112516224 A>G), RS1008615740 (4:112515291 C>A,T), RS1009014082 (4:112513519 T>A,C,G)

Disease associations

OMIM: gene MIM:606624 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

7 associations (top):

StudyTraitp-value
GCST002337_110Amyotrophic lateral sclerosis (sporadic)3.000000e-06
GCST005951_145Body mass index4.000000e-08
GCST010143_1Meat-related diet3.000000e-08
GCST010701_20Cortical surface area (MOSTest)1.000000e-242
GCST010702_74Subcortical volume (MOSTest)2.000000e-11
GCST010703_129Brain morphology (MOSTest)3.000000e-08
GCST011053_9Neuroblastoma (pediatric)2.000000e-09

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0008111diet measurement
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

36 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression2
Chir 99021affects binding, affects cotreatment, increases expression2
Tretinoinaffects cotreatment, increases expression, decreases expression2
Valproic Aciddecreases methylation, increases expression2
securininedecreases expression1
2-methyl-4-isothiazolin-3-oneincreases expression1
ascorbate-2-phosphateaffects binding, affects cotreatment, increases expression1
ethyl-p-hydroxybenzoatedecreases expression1
arseniteincreases methylation1
mono-(2-ethylhexyl)phthalateincreases expression1
doxylamine succinateincreases expression1
abrineincreases expression1
nilotinibincreases expression1
XAV939affects binding, affects cotreatment, increases expression1
LDN 193189affects cotreatment, increases expression1
theaflavin-3,3’-digallateaffects expression1
Dabigatranincreases expression1
Leflunomideincreases expression1
Abacavirincreases expression1
Air Pollutantsincreases abundance, increases expression1
Methanolincreases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Caffeineincreases expression1
Diethylhexyl Phthalatedecreases expression1
Fluorouracildecreases expression1
Folic Acidincreases expression1
Phenytoinincreases expression1
Smokeincreases expression1
Thalidomideincreases expression1

Cellosaurus cell lines

93 cell lines: 70 embryonic stem cell, 23 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_A4L5SEES3-1V human NEUROG2, clone1Embryonic stem cellMale
CVCL_A4L6SEES3-1V human NEUROG2, clone2Embryonic stem cellMale
CVCL_A4L7SEES3-1V human NEUROG2, clone3Embryonic stem cellMale
CVCL_C4EKH9 AAVS1-TRE3G-NGN2Embryonic stem cellFemale
CVCL_C4ELH9 AAVS1-TRE3G-NGN2 ATG12-/-Embryonic stem cellFemale
CVCL_C4EMH9 AAVS1-TRE3G-NGN2 PINK1-/-Embryonic stem cellFemale
CVCL_C4ENH9 AAVS1-TRE3G-NGN2 FBXO7-/-Embryonic stem cellFemale
CVCL_C7XJPre-i3Neuron NGN2 iPSC clone 1Induced pluripotent stem cellMale
CVCL_C7XKPre-i3Neuron NGN2 iPSC LRRK2-p.G2019S knock-inInduced pluripotent stem cellMale
CVCL_D1IAH9 AAVS1-TRE3G-NGN2 RETREG3-/-Embryonic stem cellFemale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.